/***************************************************************************
 *   Copyright (C) 2007 by Alexandre Masselot,,,   *
 *   alex@alex-laptop   *
 *                                                                         *
 *   This program is free software; you can redistribute it and/or modify  *
 *   it under the terms of the GNU Library General Public License as       *
 *   published by the Free Software Foundation; either version 2 of the    *
 *   License, or (at your option) any later version.                       *
 *                                                                         *
 *   This program is distributed in the hope that it will be useful,       *
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of        *
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         *
 *   GNU General Public License for more details.                          *
 *                                                                         *
 *   You should have received a copy of the GNU Library General Public     *
 *   License along with this program; if not, write to the                 *
 *   Free Software Foundation, Inc.,                                       *
 *   59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.             *
 ***************************************************************************/
#include "utils/spectraalignment.h"
#include "utils/peakintensity.h"
#include "utils/deltamassbuilder.h"
#include "utils/runlcmsmsreadermgf.h"

using namespace std;
using namespace bol;

#define STRINGIFY(x) XSTRINGIFY(x)
#define XSTRINGIFY(x) #x


int main(int argc, char **argv){
  string file=STRINGIFY(DATADIR) "/align.mgf";

  RunLcmsmsReaderMGF reader;
  RunLcmsms run;
  reader.read(run, file);
  DeltaMassBuilder deltamassbuilder;

  for(int i=0; i<run.msmsCollection().size(); i+=2){
    SpectraAlignment<PeakIntensity, PeakIntensity>
        spalign((const SpectrumLcmsms*)run.msmsCollection()[i],
                 (const SpectrumLcmsms*)run.msmsCollection()[i+1],
                  deltamassbuilder.deltamassInstance("2Da")
               );
    cout<<"------------ "<<i<<"/"<<(i+1)<<endl;
    cout<<spalign<<endl;
  }

}
